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Intro to Data Analysis

Utah Valley University - BIOL3100

Quick links:

Course GitHub Repository

Course Syllabus

Shared Course Notes

(Anyone with link can edit)

The philosophy of this course

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Table of Contents

Week 1 | Week 5 | Week 9 | Week 13

Week 2 | Week 6 | Week 10 | Week 14

Week 3 | Week 7 | Week 11 | Week 15

Week 4 | Week 8 | Week 12 | Week 16

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The Command Line, File Paths, Git

Week 1

• Topics:
• Installing Software | Command-line | Git version control
• Assignments
  
• Read: What is Git all about?
• Install Git, R, and R-Studio on your laptop (part of Assignment 1)
• Be ready to explain what Git, R, and R-Studio are.
• Do Assignment 1 and upload a link to your new GitHub account to Canvas.
• Resources
• Download Git
• Download R
• Download R-Studio
• Navigating with the command line
• Basic Git Commands
• Practice
• Make 10 separate changes and commits to your README.md file and push each one to GitHub

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Week 2

• Topics
• File paths | Pipes | Redirection | Wildcards | Essential Unix Commands | Parameters
• Assignments
• Assignment 2
• Resources
• Remedial Unix Shell
• Basic Unix Commands
• Very Useful Tutorial
• Practice
• Exercise 1
• Exercise 2

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Getting to Know R

Week 3

• Topics
• R Data types and conversions | Reading and Writing Files | For-Loops | Packages and Projects
• Assignments
• Assignment 3
• Assignment 4
• Resources
• Data Types in R
• For-Loops
• Reading data into R
• R Projects
• Practice
• Vectors
• Factors
• Characters
• Regular Sequences
• Indexing
• Missing Values
• Loops in R

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Week 4

• Topics
• Logical Operations | Subsetting | “Grammar of Graphics” ggplot Intro
• Assignments
• Read through the materials in the Resources section below
• Assignment 5
• Exam 1
• Resources
• Subsetting
• More Subsetting(It’s important!)
• Operators
• Practice
• Logical Operations
• Find a new built-in data set in R. Use several methods to subset it over and over until you are an expert!
• Out-of-order Code

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Visualizing a Data Set

Week 5

• Topics
• ggplot | patchwork | ggforce
• Assignments
• Assignment 6
• Ugly plot contest!
• Resources
• ggplot Introduction
• More ggplot
• ggforce
• patchwork
• Extensive ggplot2 Tutorial
• Practice
• Out-of-order Plotting Code
• ggplot Examples
• ggplot Shiny App Lets you use GUI to see ggplot code.

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Clean and Transform Data

Week 6

• Topics
• Tidy Data | dplyr verbs | tidyr verbs
• Assignments
• Read this paper: Tidy Data
• Assignment 7
• Resources
• Tidy Data Chapter
• Transforming Data Frames
• dplyr Verbs
• tidyr Verbs
• tidyverse Cheat Sheet
• Practice
• BioLog Challenge
• Out-of-order Code
• Out-of-order Code2

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Week 7

• Topics
• Data Wrangling | Joins | The Curse of Other Peoples’ Data
• Assignments
• Read This Handout
• Read This Paper
• Create a validated Excel Spreadsheet for data collection for the experiment we design in class
• Exam 2
• Resources
• Data Wrangling Chapter
• Wrangling Cheat Sheet
• Visual Explanations of Joins
• Practice
• Download this spreadsheet. See if you figure out all the things wrong with it.
• Error Sleuth Practice
• Data Entry Case Study

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Getting More From R

Week 8

• Topics
• Writing Functions | Conditional Execution | source()
• Assignments
• Resources
• Functions
• Conditional Execution
• Practice
• Write a function that returns the min, max, and mean of any set of real numbers
• Write a function that takes a data frame and returns a new data frame with one random column removed
• Write a function that takes a data frame… if there are more than 3 columns, your function should return the column names as-is; if there are 3 or fewer columns, your function should return the column names in reverse order.
• Write a useful function that you might want to use in the future (your choice)
• Put all of these functions into a new R script and save it in your main data course repository
• In a new empty R script, call your functions with source() and test them out

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Model Building and Testing

Week 9

• Topics
• Building and Testing Models
• Assignments
• Assignment 8
• Resources
• Modeling Intro
• Model Basics
• Model Fitting
• Practice
• Building Models Example
• Intro to Hypothesis Testing
• Cross-Validation and Logistic Regression

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Week 10

• Topics
• More models | Statistical Tests
• Assignments
• Resources
• Linear Regression
• More Linear Regression
• Common Statistical Tests
• Practice

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Communicating Your Results

Week 11

• Topics
• R-Markdown | Reproducible Reports
• Assignments
• Assignment 9
• Resources
• Intro to R Markdown
• Markdown Live Preview Generator
• Expert-Level Markdown Project
• Practice
• Using the resources above, generate a markdown document that analyzes the “iris” data set and push it to a new GitHub repository named Iris_Markdown
• Play with options and code to create a document that looks good and presents your analysis and results clearly
• This is similar to Assignment_9, but I’m asking for a brand new “Iris_Markdown” repository that is self-contained.

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Week 12

• Topics
• Proper Project Organization | Collaboration
• Assignments
• Peer evaluation of Assignment 9 (Organization, Portability, Accuracy, Understandablity)
• Exam 3
• Resources
• Project-oriented Workflows
• Reproducible, Portable, Self-Contained
• Proper Project Organization Example
• Another, More Detailed Example
• Practice
• Peer evaluations of Iris_Markdown repositories (from last week); Clean them up and make them more organized

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Putting it all together

Week 13

• Topics
• Data Analysis from raw to report
• Assignments
• We will work together in class to do a complete analysis in real-time
• Resources
• Benefits of Live Coding
• Practice
• Analyze the “esoph” data set and generate a markdown report

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Week 14

• Topics
• Building a website with GitHub and R-Markdown
• Assignments
• Work on Final Project
• Create a GitHub Personal Website
• Upload a brief CV and the updated (improved) html of Assignment 9 to your new website
• Resources
• GitHub Pages
• Here’s the GitHub repository for this course website
• Practice
• Go through my course website repository (link above) and try to relate the code there to the html version of the website your internet browser is displays

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Week 15

• Topics
• TBD
• Assignments
• Work on Final Project

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Week 16

• Topics
• TBD
• Assignments
• Exam 4 (Redo any previous exam to replace it’s score)

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